Fortinbras blog
Welcome to Fortinbras Research.
latest
spaTyper has been completely
refactored and the spatype database updated. Please update your bookmarks to
the new url
http://spatyper.fortinbras.us
Users should see faster processing times and regular updates
of the spa type database. The refactor will make maintenance and
addition of new features easier. Please contact me if you experience any
issues with this new version.
spaTyper is now powered by
Mojolicious!
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 26 Oct 2013
I've fixed a major bug that was resulting in different score averages
for degenerate sequences depending on whether "Average score" or "Full
expansion" was selected. The scores are now the same and correct for
both selections. A sequence type selector has also been added: when too
many ambiguities are present in a nucleotide sequence, the code can
wrongly interpret the sequence as "amino acid". The control forces the
selected interpretation regardless of the residues present in the sequence.
I apologize for any inconvenience these bugs may have caused users.
Many thanks to the group at U. Roma "Tor Vergata" for catching
this bug, and sending test data to work it out.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 03 Dec 2009
bioperl-max,
v0.1.2 is available, with Amazon Machine Image
id
ami-1ad03273. Newly installed are the short-read
assembly tools
bwa,
maq,
and
samtools. Bioperl
packages
bioperl-live and
bioperl-run are
updated to r16427, and contain maq, bwa, and samtools support.
Fortinbras maintains this AMI as a free service to the research community. Check
out
Amazon Web Services to get
started in the cloud. Happy coding!
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 28 Nov 2009
The
spaTyper repeat
and
spa database has been completely updated. 329 repeat
sequences and 5719 known
spa types are now recognized. I
appreciate the use
spaTyper has been getting in recent
weeks. If you find it useful, please tell your colleagues, and let me
know how I can improve it.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 20 Sep 2009
A gene filtering and clipping feature has been added
to
HIVQuery. This has been
implemented as a post-processing step after the initial query has been
run, when the user makes download format selections. Details can be
found on the
help
page. Many thanks to David Posada for this suggestion.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 09 Aug 2009
bioperl-max,
v0.1.1 is available, with Amazon Machine Image
id
ami-b55dbbdc. Newly installed
are a git clone of
perl6 (Rakudo) and
svn revision r39729
of
parrot.
NeXML
is updated to r1136,
and
bioperl-live
to r15800. Fortinbras maintains this AMI as a free
service to the research community. Check
out
Amazon Web Services to get
started in the cloud. Happy coding!
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 23 Jun 2009
We've added a
page containing links to Fortinbras resources beyond the
public applications. Please have a look.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 11 Jun 2009
bioperl-max is
a 32-bit Ubuntu Hardy(8.04)-based Amazon Machine Image (AMI), fully
loaded with the BioPerl production packages
(
bioperl-live,
bioperl-db/biosql,
and
bioperl-run), along with a large variety of open-source
bioinformatics tools. The tools include popular apps
like
blast,
hmmer, and
HyPhy, as well as R
and the GNU compiler suite. Fortinbras maintains this AMI as a free
service to the research community. Check
out
Amazon Web Services to get
started in the cloud.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 10 Jun 2009
HIVQuery has been updated with
new options for data retrieval.
Besides FASTA formatted sequences and
annotations, users can now retrieve annotations in XML, valid against
http://fortinbras.us/HIVDBSchema/1.0. This
is a set of XML Schema definitions designed by Fortinbras that
represent the underlying structure of
the
Los
Alamos HIV Sequence Database. The
.xsd files can be
obtained directly from the HIVDBSchema/1.0 URL.
Sequence data can also now be obtained
in
NeXML format, an emerging XML
standard for evolutionary data exchange. Details on NeXML can be
obtained at http://www.nexml.org, and extensive technical discussion
is available
at
NESCent's
EvoInfo
Working Group wiki.
There has been a rationalization of the query interface. A single
button now runs a query. Following the run, the user is
presented with data download options.
Please
notify me of any issues
that arise with these experimental features.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 11 Apr 2009
The
HIV coreceptor predictor
now allows the use of the improved cutoff scores described in
Poveda, Seclén,
González, et al 2009. These cutoffs were shown to improve
predictor performance with respect to virus phenotypes emerging under
Maraviroc therapy in the ALLEGRO trial. Please cite this paper if you
publish results using this predictor.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 24 Mar 2009
The
HIV coreceptor predictor
has been updated. When expanding degenerate sequences (sequences
containing ambiguity symbols), there is now an option for reporting
just the average score over all sequences in the expansion, without
returning each disambiguated sequence separately. Returning the
average only is a comparatively fast calculation, so the program
will analyze sequences representing up to 16384 combinations. The
option to return and score each combination separately is still
available, with the previous limit of 512 combinations. See the
updated
help
page for more details.
Other efficiencies have been added and minor bugs fixed.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 27 Feb 2009
Recently on
EVOLDIR,
Gavin Gouws at the
South African
Institute for Aquatic Biodiversity put out a distress call regarding
an old phylogenetic analysis program,
BIOSYS2. This
program, in FORTRAN, was apparently the ancestor of
PAUP. I tweaked the source,
fixed some bugs, and increased the array dimensions to work with modern
datasets. A Windows stand-alone executable, compiled with
GNU FORTRAN
under
Cygwin, is
available here.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 05 Feb 2009
The
HIV coreceptor predictor
has been updated with new features. It can now handle degenerate
nucleotide sequences (those
containing
IUPAC
ambiguity symbols). The tool will automatically analyze all
possible unamibiguous amino-acid sequences implied by the ambiguities
present in the input sequences. Each amino acid sequence is displayed
and scored; the average score (and prediction for that average) over
all possible combinations is also reported. Thanks to a French
colleague for this valuable suggestion.
The V3 loop search options have also been rationalized, and a bug or
two fixed. For an overview of the new features, see the
preprocessing
help page.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 03 Feb 2009
The web-based interface to
HIVQuery seems to be working well as of the
time of this post. The ISP,
Network
Solutions, has been working behind the scenes; many thanks to them.
Fixes in annotation slurping are working as well. Enjoy-
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 01 Feb 2009
A
sequence query
tutorial is now available. It briefly describes the idea of querying
databases, and gives details and examples for writing HIVQuery-style
queries. Thanks to colleagues in The Netherlands for the suggestion!
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 30 Jan 2009
hivq.PL has been updated. The distribution options now
include a Windows executable, containing everything necessary to run
HIVQuery without a separate Perl interpreter.
Significant bug fixes have also been made on the underlying module
Bio::DB::Query::HIVQuery; in particular, problems with retrieving
annotations have been fixed. These changes have been committed to the
BioPerl trunk,
called
bioperl-live.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 28 Jan 2009
The
BioPerl 1.6 stable release is
now available. It contains HIVQuery modules and many, many other
goodies. Visit
the
release page.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 25 Jan 2009
Command-line queries for the HIV DB
hivq.PL is a Perl script that allows
command-line query and retrieval of HIV sequences from
the Los Alamos HIV DB. If you can run Perl, you should
be able to run the script. It depends on a number of
BioPerl modules, which
are packaged with the
hivq.PL
distribution.
Download it in
Linux and Windows flavors.
hivq.PL uses BioPerl version 1.6. If you want
the whole toolkit (and why not?)
visit
here
and
here.
Your feedback is very important. As always,
contact us
with bug reports and enhancement suggestions.
MAJ 24 Jan 2009
Looks like the timeouts are on the Fortinbras side. Los
Alamos has responded extremely helpfully with an access log
snippet showing that Fortinbras queries are completed
successfully on their end, and reiterated that there are no
blocked IPs for any reason at this time.
Look for a
downloadable command-line-based script
here in the coming
days that will run on your local machine. In the meantime,
we'll continue to pursue the CGI problem.
As
always,
contact us
with bug reports and enhancement suggestions.
MAJ 21 Jan 2009
HIVQuery continues to time out in its requests to the
The
Los
Alamos HIV Sequence Database. I have had a response
from LANL saying that there shouldn't be a problem with
an external user agent accessing the site. I suspect
that an automatic block was issued for some reason, and
I am pursuing the removal of this.
In the meantime, since running HIVQuery from elsewhere
appears to work fine, I am planning to write simple CGI
script that will provide the functionality that the
Fortinbras tool provides. This will be made available
in the examples directory of the BioPerl trunk. If that
doesn't mean anything to you, no problem, I will also
put it up on the Fortinbras site. This should work for
you, if you have the ability to run a webserver like
Apache. (And, everyone does; that I will attempt to
describe in the installation instructions.)
Watch this space for further releases and updates.
As always,
contact
us with bug reports and enhancement suggestions.
MAJ 18 Jan 2009
The good news: HIVQuery has been updated to use the new
The
Los
Alamos HIV Sequence Database schema and passes all
tests. The bad news: requests to LANL from Fortinbras are
timing out. I am waiting for a response from the LANL DB adminstrators
to see what can be worked out. Watch this space.
As always,
contact
us with bug reports and enhancement suggestions.
MAJ 15 Jan 2009
The
Los
Alamos HIV Sequence Database has been performing
key updates. This may result in some changes to the
underlying structure. I am working to make sure that
HIVQuery stays compliant with the LANL interface. There
may be odd errors and failed requests over the next
couple of days, but I hope to have these sorted out by
the end of this week.
Thank you for the continuing interest in HIVQuery, and your
patience.
As always,
contact
us with bug reports and enhancement suggestions.
MAJ 14 Jan 2009
The BioPerl modules underlying
HIVQuery have been
updated with the critical fix from the last post
in the
BioPerl
Subversion
repository.
To access Release Candidate 2 of the upcoming BioPerl 1.6
release, run the following command
$ svn co svn://code.open-bio.org/bioperl/bioperl-live/branches/branch-1-6 bioperl-1-6
As always,
contact
us with bug reports and enhancement suggestions.
MAJ 04 Jan 2009
HIVQuery Major Update
HIVQuery has been updated. Critical fix allows
all tables
(see
valid
fields and tables) to be joined transparently to the user.
Major new features: user can view the LANL response HTML
page when searches fail, convenience links to GenBank
entries added to FASTA HTML output.
As always,
contact
us with bug reports and enhancement suggestions.
MAJ 03 Jan 2009
spaTyper Major Update
spaTyper has been updated. Major features: automatic
reverse complement search, html and plain text results
format, sequence coordinates included in repeat inspector
(correctly calculated for forward and reverse directions),
full documentation, unified visual design.
As always,
contact
us with bug reports and enhancement suggestions.
MAJ 03 Jan 2009
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MAJ 02 Jan 2009